8-11485477-C-G

Variant names:

• chr8-11485477-C-G
• rs2254660

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.828 in 152,166 control chromosomes in the GnomAD database, including 52,350 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52350 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125888 AN: 152048 Hom.: 52299 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.820

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.828 AC: 125996 AN: 152166 Hom.: 52350 Cov.: 31 AF XY: 0.820 AC XY: 61008 AN XY: 74372

African (AFR) AF: 0.860 AC: 35678 AN: 41508

American (AMR) AF: 0.846 AC: 12947 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2882 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3816 AN: 5164

South Asian (SAS) AF: 0.791 AC: 3809 AN: 4816

European-Finnish (FIN) AF: 0.692 AC: 7319 AN: 10574

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56946 AN: 68020

Other (OTH) AF: 0.822 AC: 1733 AN: 2108

Alfa AF: 0.812 Hom.: 2518

Bravo AF: 0.850

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.17
PhyloP100		-0.089

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2254660; hg19: chr8-11342986;